The health of the Great Barrier Reef is declining and requires an urgent "net benefit policy" to ensure development along the Queensland coast does no further damage to the vast coral ecosystem, according to a major government assessment.

The Great Barrier Reef strategic assessment warns that the reef faces numerous threats, including erosion of water quality, a plague of crown-of-thorns starfish and climate change, which is described as the "most serious long-term risk facing the reef".

The Great Barrier Reef Marine Park Authority's report, which analysed the health of the World Heritage-listed marine park area, identified the need to reduce sediment, nitrogen and nutrient flows onto the reef. A parallel report, conducted by the Queensland government, looked at the condition of the coastline alongside the Great Barrier Reef.

The marine park assessment states that "urgent and effective" intervention is required. It proposes that a "net benefit policy" should ensure coastal activities produce an overall benefit to the reef, with more focus on the overall impact of human activities and weather events such as cyclones, rather than individual events.

It paints a stark picture of the health of the reef, which has lost about half of its coral cover in the past 30 years, with the southern portion of the 2,300km long ecosystem faring particularly badly.

"Unsustainable practices – some dating back more than a century – combined with the last 10 years of extreme weather have affected the ecosystem and reduced its ability to recover from disturbance," the report states.

"This is especially true for inshore areas adjacent to the more developed part of the catchment. For some species, such as dugongs and inshore dolphins, and some habitats, such as coral reefs and sea grass meadows, their condition in this area is assessed as poor or very poor and declining.

"Water quality in the region has declined markedly, especially in inshore areas adjacent to the developed coast."

There are nine species within the Great Barrier Reef marine park considered "highly vulnerable" in the report, including dugongs, dolphins, sharks, seabirds and fish such as salmon and snapper.

There are few examples of recovering populations of reef species, the report reveals, with full recovery of species "likely to take decades".

Overall, the health of the reef is "declining", with climate change posing "far reaching" future challenges for the ecosystem, according to the report.

"Future climate change predictions indicate sea level rises and temperature increases will continue and the ocean will become gradually more acidic," it states. "Extreme weather events are predicted to increase in severity. These changes will have dramatic effects on the health and resilience of the reef."

The assessment of the reef's health was called for by Unesco's world heritage committee in June, which warned that it will place the prized asset on its "in danger" list next year unless improvements were made in water quality and curbing the scope of development along the Queensland coast.

Conservationists have called for a halt to major port expansion – such as Abbot Point near the town of Bowen – due to the damage caused by the dredging and dumping of seabed sediment. The government assessment states the redistribution of seabed material is a "key concern".

Felicity Wishart, campaign director at the Australian Marine Conservation Society, told Guardian Australia she was disappointed there was no commitment to reduce the scope of coastline development.

"It's clear the reef is in dire straights, especially the southern two thirds," she said. "We agree that further work needs to be done to improve water quality but we can't afford to make the situation worse and there's no commitment here to do anything other than tweak business as usual.

"Despite all of the scientific evidence, the Queensland government has said Abbot Point will go ahead. There is a head-in-the sand attitude towards the reef. The current approach needs to change and politicians can't wash their hands of this.

"There is very little rationale to progress developments at this speed at a time when there's been a slowdown in the mining industry. I really expected more leadership in this document."

Greg Hunt, the environment minister, is set to make a decision on whether to allow the dredging of sediment to allow the expansion of Abbott Point.

Nick Heath, WWF Australia spokesman, said the strategic assessment's findings appear to give "no room" for Hunt to approve the dredging and dumping of sediment in the Great Barrier Reef marine park, as was initially proposed.

"With the reef in such a state already, often as a result of fertiliser pollution, it makes absolutely no sense whatsoever to dump in reef waters," he said.

Hunt called the protection of the reef "vital" and stressed his commitment to its preservation.

"Everyone wants to see the reef remain one of the most biologically diverse places on the planet so it can be enjoyed by future generations," he said.

"Having long-term actions and partnerships in place for tackling the challenges facing the reef help to provide greater certainty for the community, industry and the environment."

The federal government has already announced its Reef 2050 plan, which aims to improve the water quality of the reef and tackle the spread of crown-of-thorns starfish, which devour healthy coral.

The strategic assessment will now be open for public comment until 31 January.